{"id":"https://openalex.org/W2079914556","doi":"https://doi.org/10.1186/1471-2105-15-166","title":"On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation","display_name":"On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation","publication_year":2014,"publication_date":"2014-06-02","ids":{"openalex":"https://openalex.org/W2079914556","doi":"https://doi.org/10.1186/1471-2105-15-166","mag":"2079914556","pmid":"https://pubmed.ncbi.nlm.nih.gov/24890864"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-166","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-166","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-166","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-166","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026949619","display_name":"Wing\u2010Cheong Wong","orcid":"https://orcid.org/0000-0003-1247-6279"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Wing-Cheong Wong","raw_affiliation_strings":["Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore. wongwc@bii.a-star.edu.sg","Bioinformatics Institute (BII), Agency for Science, Technology and Research (A\u2217STAR), Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore. wongwc@bii.a-star.edu.sg","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A\u2217STAR), Singapore, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019975803","display_name":"Sebastian Maurer\u2010Stroh","orcid":"https://orcid.org/0000-0003-0813-9640"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Sebastian Maurer-Stroh","raw_affiliation_strings":["Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore","School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore","Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore","School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074249721","display_name":"Birgit Eisenhaber","orcid":"https://orcid.org/0000-0002-2910-7384"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Birgit Eisenhaber","raw_affiliation_strings":["Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore","Bioinformatics Institute (BII), Agency for Science, Technology and Research (A\u2217STAR), Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A\u2217STAR), Singapore, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007579711","display_name":"Frank Eisenhaber","orcid":"https://orcid.org/0000-0002-9599-5420"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Frank Eisenhaber","raw_affiliation_strings":["Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore","Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore, 117597, Singapore","School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore","School of Computer Engineering (SCE), Nanyang Technological University (NTU), Singapore, Singapore","Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore, Singapore","Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore, 117597, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Engineering (SCE), Nanyang Technological University (NTU), Singapore, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5026949619"],"corresponding_institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5691,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.67385312,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"15","issue":"1","first_page":"166","last_page":"166"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5591999888420105,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.5591999888420105,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.07400000095367432,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.05260000005364418,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.6683538556098938},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6192263960838318},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5674811601638794},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5030760169029236},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.4870660603046417},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.46438348293304443},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45308980345726013},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4326293468475342},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.42652663588523865},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41756880283355713},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.34933850169181824},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31633812189102173},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.24311470985412598},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1412586271762848}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.6683538556098938},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6192263960838318},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5674811601638794},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5030760169029236},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.4870660603046417},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.46438348293304443},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45308980345726013},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4326293468475342},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.42652663588523865},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41756880283355713},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34933850169181824},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31633812189102173},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.24311470985412598},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1412586271762848},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-15-166","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-166","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-166","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24890864","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24890864","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/174303","is_oa":false,"landing_page_url":"https://scholarbank.nus.edu.sg/handle/10635/174303","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Unpaywall 20200831","raw_type":"Article"},{"id":"pmh:oai:dr.ntu.edu.sg:10356/103901","is_oa":true,"landing_page_url":"http://hdl.handle.net/10220/20043","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4061105","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4061105","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-166","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-166","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-166","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.6899999976158142,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322193","display_name":"Nemzeti Kutat\u00e1si \u00e9s Technol\u00f3giai Hivatal","ror":"https://ror.org/03g2am276"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2079914556.pdf","grobid_xml":"https://content.openalex.org/works/W2079914556.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W204050705","https://openalex.org/W292775947","https://openalex.org/W644874088","https://openalex.org/W1014117969","https://openalex.org/W1484097762","https://openalex.org/W1513332069","https://openalex.org/W1522556730","https://openalex.org/W1534369246","https://openalex.org/W1708293692","https://openalex.org/W1740355754","https://openalex.org/W1774728382","https://openalex.org/W1902542940","https://openalex.org/W1960000138","https://openalex.org/W1965736046","https://openalex.org/W1974696436","https://openalex.org/W1977922844","https://openalex.org/W1984289421","https://openalex.org/W1989325752","https://openalex.org/W1994780992","https://openalex.org/W1996112765","https://openalex.org/W1996351562","https://openalex.org/W1999340580","https://openalex.org/W1999531492","https://openalex.org/W2001910815","https://openalex.org/W2005313213","https://openalex.org/W2008116827","https://openalex.org/W2010589579","https://openalex.org/W2022341771","https://openalex.org/W2024503898","https://openalex.org/W2032986841","https://openalex.org/W2036939278","https://openalex.org/W2041076979","https://openalex.org/W2055193239","https://openalex.org/W2061190458","https://openalex.org/W2062808129","https://openalex.org/W2064368562","https://openalex.org/W2068168838","https://openalex.org/W2068972095","https://openalex.org/W2069992928","https://openalex.org/W2074706385","https://openalex.org/W2082418604","https://openalex.org/W2082667898","https://openalex.org/W2086586192","https://openalex.org/W2088597842","https://openalex.org/W2093311325","https://openalex.org/W2097059553","https://openalex.org/W2097382368","https://openalex.org/W2099029075","https://openalex.org/W2101783948","https://openalex.org/W2105291717","https://openalex.org/W2107251251","https://openalex.org/W2108836454","https://openalex.org/W2113941718","https://openalex.org/W2114946482","https://openalex.org/W2115137312","https://openalex.org/W2117813757","https://openalex.org/W2120772351","https://openalex.org/W2121520117","https://openalex.org/W2123194031","https://openalex.org/W2123278426","https://openalex.org/W2133787379","https://openalex.org/W2134920535","https://openalex.org/W2137722843","https://openalex.org/W2141885858","https://openalex.org/W2148047088","https://openalex.org/W2152326664","https://openalex.org/W2158714788","https://openalex.org/W2166206278","https://openalex.org/W2166577446","https://openalex.org/W2170163556","https://openalex.org/W2344156640","https://openalex.org/W2905538300","https://openalex.org/W2991631909","https://openalex.org/W4210623056"],"related_works":["https://openalex.org/W2161189461","https://openalex.org/W2972635466","https://openalex.org/W4313549133","https://openalex.org/W2803517106","https://openalex.org/W4240507550","https://openalex.org/W1967142621","https://openalex.org/W2926533301","https://openalex.org/W1994428965","https://openalex.org/W2106830745","https://openalex.org/W2161062388"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"sequence":[2,23,38,90,189],"similarities":[3],"to":[4,64,74,117,219,247],"any":[5],"types":[6],"of":[7,28,67,77,84,112,151,223,231,238],"non-globular":[8],"segments":[9],"(coiled":[10],"coils,":[11],"low":[12],"complexity":[13],"regions,":[14,16],"transmembrane":[15],"long":[17],"loops,":[18],"etc.":[19],"where":[20],"either":[21],"positional":[22],"conservation":[24],"is":[25,61,93,180,211],"the":[26,96,100,103,109,119,137,152,156,193,229,236,265],"result":[27,83],"a":[29,82,113,133,205,220],"very":[30],"simple,":[31],"physically":[32],"induced":[33],"pattern":[34],"or":[35],"rather":[36],"integral":[37],"properties":[39],"are":[40,42,72],"critical)":[41],"pertinent":[43],"sources":[44],"for":[45,107,132,160,187,196],"mistaken":[46],"homologies.":[47],"Regretfully,":[48],"these":[49,68],"considerations":[50],"regularly":[51],"escape":[52],"attention":[53],"in":[54,182,228,235],"large-scale":[55,221],"annotation":[56,79],"studies":[57],"since,":[58],"often,":[59],"there":[60],"no":[62],"substitute":[63],"manual":[65],"handling":[66],"cases.":[69],"Quantitative":[70],"criteria":[71],"required":[73],"suppress":[75],"events":[76],"function":[78],"transfer":[80],"as":[81,264],"false":[85,254],"homology":[86,91,135,186,261],"assignments.":[87],"RESULTS:":[88],"The":[89,215],"concept":[92,195],"based":[94,207],"on":[95,146,208],"similarity":[97,121,242],"comparison":[98],"between":[99,267],"structural":[101,200],"elements,":[102],"basic":[104],"building":[105],"blocks":[106],"conferring":[108],"overall":[110],"fold":[111],"protein.":[114],"We":[115,167],"propose":[116],"dissect":[118],"total":[120],"score":[122,139],"into":[123,164],"fold-critical":[124,248],"and":[125,129,177,225,234,249,269],"other,":[126],"remaining":[127],"contributions":[128,251],"suggest":[130],"that,":[131,272],"valid":[134],"statement,":[136],"fold-relevant":[138],"contribution":[140],"should":[141],"at":[142],"least":[143],"be":[144],"significant":[145],"its":[147],"own.":[148],"As":[149],"part":[150],"article,":[153],"we":[154,202],"provide":[155],"DissectHMMER":[157,170],"software":[158],"program":[159],"dissecting":[161],"HMMER2/3":[162,172],"scores":[163,173],"segment-specific":[165],"contributions.":[166],"show":[168],"that":[169,178,204],"reproduces":[171],"with":[174,245],"sufficient":[175],"accuracy":[176],"it":[179],"useful":[181],"automated":[183],"decisions":[184],"about":[185],"instructive":[188],"examples.":[190],"To":[191],"generalize":[192],"dissection":[194,206,244],"cases":[197],"without":[198],"3D":[199],"information,":[201],"find":[203],"alignment":[209],"quality":[210],"an":[212],"appropriate":[213],"surrogate.":[214],"approach":[216],"was":[217,275],"applied":[218],"study":[222],"SMART":[224],"PFAM":[226],"domains":[227],"space":[230,237],"seed":[232],"sequences":[233],"UniProt/SwissProt.":[239],"CONCLUSIONS:":[240],"Sequence":[241],"core":[243],"regard":[246],"other":[250],"systematically":[252],"suppresses":[253],"hits":[255],"and,":[256],"additionally,":[257],"recovers":[258],"previously":[259],"obscured":[260],"relationships":[262],"such":[263],"one":[266],"aquaporins":[268],"formate/nitrite":[270],"transporters":[271],"so":[273],"far,":[274],"only":[276],"supported":[277],"by":[278],"structure":[279],"comparison.":[280]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
